FROM tomcat:9-jdk17-temurin-focal

ARG USER_ID
ARG GROUP_ID

RUN apt-get update && apt-get install -y sudo;

RUN addgroup --gid ${GROUP_ID} labkey
RUN adduser --gecos 'LabKey' --uid ${USER_ID} --gid ${GROUP_ID} --disabled-password labkey 
RUN echo 'labkey ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
RUN usermod -G root,sudo labkey

USER labkey

ARG RKEY=https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc 
ARG GPGKEY=/etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
RUN sudo apt-get update \
   & sudo apt-get install -y dirmngr gnupg apt-transport-https ca-certificates software-properties-common wget\
	&& wget -qO- $RKEY | sudo tee -a $GPGKEY\
	&& sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/"\
	&& sudo apt-get update --fix-missing\
	&& sudo apt-get install -y r-base \
	&& sudo rm -rf /var/lib/apt/lists/*

#prepare directory where files will be mapped 
RUN sudo mkdir -p /data/labkey && \
	sudo chown -R labkey:labkey /data/labkey && \
	sudo chown -R labkey:labkey /usr/local/tomcat 

#install (labkey local) R packages and dependencies
RUN mkdir -p /home/labkey/R/site-library \
	&& sudo apt-get update\
   && sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev  libharfbuzz-dev libfribidi-dev libtiff5-dev \
   && export R_LIBS=/home/labkey/R/site-library \
   && echo ${R_LIBS} \
   && R -e 'install.packages(c("devtools","ggplot2","Rlabkey"))'


#RUN sudo mkdir /usr/local/labkey \
#   && sudo chown -R labkey:labkey /usr/local/tomcat \
#   && sudo chown -R labkey:labkey /usr/local/labkey
#USER root

LABEL "name"="tomcatLabkeyR"